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== Port applications to Dutch Life Science Grid ==
'''People'''
* AMC: Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos
* Sara/BiGGrid: Tom Visser
* UMCG: Morris Swertz, Freerk van Dijk

=== Description ===
Software is being implemented as workflow components. The workflows will run on the Dutch life science grid.

* [http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/ Information about the infrastructure]
* [http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/GettingStarted Getting started]
* Angela CM Luyf, Barbera DC van Schaik, Michel de Vries, Frank Baas, Antoine HC van Kampen, Silvia D Olabarriaga (2010) '''Initial steps towards a production platform for DNA sequence analysis on the grid.''' BMC Bioinformatics 11: 1. Dec [http://www.ncbi.nlm.nih.gov/pubmed/21156038 pubmed] 

=== Data access rights ===

To ensure that the most limited group of people has access to the data we have created a subgroup "gvnl" within the "vlemed" Virtual Organisation (VO).
For people to become part of this group, it is required that they have a Grid certificate and that they are part of the "vlemed" VO.
On the following page there is information on how to get a certificate, how to get into the "vlemed" VO: http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/EBioInfra#Access

[http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/DataManagement More information about data access]

== Data location on grid ==

=== Data ===

The data is located on the grid storage and only readable and writable for the vlemed/gvnl group.

Storage location (LFC resource): lfc.grid.sara.nl

Path: /grid/vlemed/gvnl/data

URI: lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl

=== Workflows and databases ===

* [BigComputeTemplates Implemented workflows]

These directories are open to all members of the vlemed VO

* Workflows: lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF
* Databases: lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_DB

The directories that contain the workflows have the following structure:
|| '''Directory''' || '''Description''' ||
|| bin || dependent binaries like bwa, samtools ||
|| GasW || component description, describes which executable has to run on grid and it specifies the in and output files/parameters ||
|| Java || dependent jar files, e.g. the GATK jar ||
|| parameterFiles || text files that contain exactly one line with the parameters that you would like to provide to bwa or another component ||
|| Scufl || old workflow description files, can be ignored ||
|| shFiles || these files are executed on the grid and described by the GASW descriptor, the gvnl shFiles are based on the Groningen templates ||
|| Workflows || Workflow descriptions, clicking on them will start the Moteur plugin. Input files/parameters can be specified in the fields. If you click on "Run" the jobs are submitted to the grid ||

The shell files can (in most cases) run on any linux cluster. In that case you need to place the shell file and the dependent executable(s) in one directory. At the start of each shell file is an example on how to run them.

== Alternatives ==

=== Clusters ===

* Groningen (Freerk)
* Utrecht (Ies)
* Rotterdam (Slavik)
* Leiden (Jeroen)
* Huygens (Jan)
* Lisa
* Philips (is one of the grid sites)
* DAS

=== Grid ===

* [http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/ EBioInfra]
* [http://www.cloud.sara.nl/ BiGGrid Cloud]
* [https://grid.sara.nl/wiki/index.php/Using_the_Grid/ToPoS Topos]